taylo5jm / hsds

Data science study group at HemoShear Therapeutics

HemoShear Data Science Study Group

Installing software

Install brew (Mac only)

brew is a package manager for OS X. Press Command + Spacebar and type terminal to open a command prompt, and paste the following line:

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Install git

git is a version control system. This is a great tool that allows us to collaborate on projects. If you installed brew on a Mac, you should also have git. If you are on a PC, install git for Windows.

Clone this git repository

After you have installed git, it is a good idea to make a new directory for your work. Start out somewhere like /Documents and make a new directory from there:

mkdir DataScience
cd Documents

After you are in a new directory, clone the repository. clone is the git command for retrieving an entire copy of a repository from a remote source.

git clone https://github.com/taylo5jm/hsds

You can do ls now to see that there is a directory called hsds. This is the git repository that you just cloned. We can change directories to hsds.

cd hsds

In this directory, there is a Dockerfile, which is a set of instructions for building our custom RStudio computing environment. To install our curstom RStudio Server version, we can build a Docker image with the Dockerfile in our repository. In the line below, docker build is telling the machine to run the build command in docker. -t is an option that is short for tag, so -t hs-rstudio will tag the image as hs-rstudio, a name we can recognize and possibly remember. The . at the end tells docker to look in our current directory.

docker build -t hs-rstudio .

The image can take up to 30 minutes to build. After this process is complete, you can run RStudio with the following line:

docker run -d -p 8787:8787 hs-rstudio

You should see a long string of random numbers and letters. If not, something is wrong. At this point, you can go to localhost:8787 in your browser and sign in to RStudio with the username and password rstudio.

You can make files in this new container, but when the container is stopped, any data will cease to exist. You can map a volume to a container with the -v option. -v /Users/justin/Documents/data:/data will expose any data in /Users/justin/Documents/data on my machine to /data in the container.

docker run -d -p 8787:8787 -v /Users/justin/Documents/data:/data hs-rstudio